Profiling Condition-Specific, Genome-Wide Regulation of mRNA Stability in Yeast

Barrett C. Foat, S. Sean Houshmandi†, Wendy M. Olivas†, and Harmen J. Bussemaker‡§

*Department of Biological Sciences, Columbia University, New York, New York 10027, U.S.A.
†Department of Biology, University of Missouri–St. Louis, St. Louis, Missouri 63121, U.S.A.
‡Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, U.S.A.
§Corresponding author: Harmen.Bussemaker@columbia.edu

Supporting Material

Supporting Data

Position Specific Affinity Matrices (PSAMs)

The weight values for the six PSAMs detailed in the paper plus the two with fewer significant hybridizations are available as perl Data::Dumper strings, as flat tab-delimited text files, or as logo images.

Trans-factor Activity Profiles (TFAPs)

TFAPs are available in tab-delimited text files as either the regression coefficients or as t-values corresponding to those regression coefficients.

Set	t-values	coefficients
All 758 pairs of experimental conditions for all discovered PSAMs	ts	Fs
Gerber affinity selection data for the six reported PSAMs	ts	Fs
Grigull transcriptional arrest puf4 deletion vs. wild-type for the P4E	ts	Fs

In addition, the t-value TFAPs over all the conditions can be browsed graphically by loading this *.cdt file into the TreeView application (cited below).

Target Genes

The target genes for each PSAM are available in tab-delimited text files. If the PSAM corresponded to a Puf protein from Gerber et al., 2004 or a 3' Motif from Kellis et al., 2003, it is annotated in the file along with their common targets.

PSAM Matches

The sequences and locations of PSAM matches within their target genes' downstream sequences are available in text tables.

Sequence Data

The non-redundant downstream 200 nucleotide set that was used for the PSAM discovery and the downstream 400 nucleotide set that was used for Responder Analysis are available in fasta format.

Expression Data

All of the expression data used for this study are published, available on the internet, and listed on either the Stanford MicroArray Database or the Yeast MicroArray Global Viewer.

Software

Xiang-Jun Lu has created a partially reimplemented, pure C language version of MatrixREDUCE for distribution. He has also added a number of convenient features and supporting scripts. The free software download for non-commercial use is available at http://www.bussemakerlab.org/software/MatrixREDUCE/.

For hierarchical clustering of TFAPs between PSAMs, we recommend Cluster 3.0:
M. J. L. de Hoon, S. Imoto, J. Nolan, and S. Miyano: Open Source Clustering Software. Bioinformatics, 20 (9): 1453-1454 (2004).
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/index.html
Cluster was not intended for use on TFAPs, but it works well as long as you remember that "Genes" refers to experimental conditions and "Arrays" refers to PSAMs for the MatrixREDUCE output.

For visualization of clustered PSAMs, we recommend Java TreeView:
Alok J. Saldanha: Java TreeView—extensible visualization of microarray data. Bioinformatics, 20 (17): 3246-3248 (2004).
http://jtreeview.sourceforge.net/